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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Fusion and fission events regulate endosome maturation and viral escape

Endosomes are intracellular vesicles that mediate the communication of the cell with its extracellular environment. They are an essential part of the cell’s machinery regulating intracellular trafficking via the endocytic pathway. Many viruses, which in order to replicate require a host cell, attach themselves to the cellular membrane; an event which usually initiates uptake of a viral particle through the endocytic pathway. In this way viruses hijack endosomes for their journey towards intracellular sites of replication and avoid degradation without host detection by escaping the endosomal compartment. Recent experimental techniques have defined the role of endosomal maturation in the ability of enveloped viruses to release their genetic material into the cytoplasm. Endosome maturation depends on a family of small hydrolase enzymes (or GTPases) called Rab proteins, arranged on the cytoplasmic surface of its membrane. Here, we model endosomes as intracellular compartments described by two variables (its levels of active Rab5 and Rab7 proteins) and which can undergo coagulation (or fusion) and fragmentation (or fission). The key element in our approach is the “per-cell endosomal distribution” and its dynamical (Boltzmann) equation. The Boltzmann equation allows us to derive the dynamics of the total number of endosomes in a cell, as well as the mean and the standard deviation of its active Rab5 and Rab7 levels. We compare our mathematical results with experiments of Dengue viral escape from endosomes. The relationship between endosomal active Rab levels and pH suggests a mechanism that can account for the observed variability in viral escape times, which in turn regulate the viability of a viral intracellular infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3

Abstract Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic and diseases caused by other coronaviruses.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Global characterization of biosynthetic gene clusters in non-model eukaryotes using domain architectures

Abstract The majority of pharmaceuticals are derived from natural products, bioactive compounds naturally synthesized by organisms to provide evolutionary advantages. Although the rich evolutionary history of eukaryotic algal species implicates a high potential for natural product-based drug discovery, it remains largely untouched. This study investigates 2762 putative biosynthetic gene clusters (BGCs) from 212 eukaryotic algal genomes. To analyze a vast set of structurally diverse BGCs, we employed comparative analysis based on the vectorization of biosynthetic domains, referred to as biosynthetic domain architecture (BDA). By characterizing core biosynthetic machineries through BDA, we identified key BDAs of modular BGCs in diverse eukaryotes and introduced 16 candidate modular BGCs with similar BDAs to previously validated BGCs. This study provides a global characterization of eukaryotic algal BGCs, offering an alternative to laborious manual curation for BGC prioritization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Neutrons reveal the dynamics of leaf thylakoids in living plants

The study is the first known exploration of photosynthetic membranes dynamics in living plants by high resolution quasielastic neutron scattering spectroscopy. We investigated the mobility and flexibility of thylakoid membranes in common duckweed (Landoltia punctata) and identified dynamics across various length scales corresponding to individual membranes and membranes stack. We employed classical models typically used to study lipid bilayers to characterize the undulation modes and rigidity of the membranes and reveal how structural variations influence the observed complex dynamics. Our findings show that the stacks of thylakoids in duckweed behave as rigid systems, exhibiting an effective bending coefficient in the lower range associated with surfactant membranes. In contrast, the single thylakoid leaflets display greater apparent flexibility and are well situated within the bi-continuous surfactant phase dynamics. While our observations enhance the understanding of the intricate architecture and mobility of photosynthetic cellular machinery, they also highlight the limitations of applying ideal lipid membranes models to describe complex biological systems. This work opens more questions and the need for further investigations across extended length and time scales, as well as the importance of rigorous sample preparation and experimental control.

Applied physics↗
DOE OSTI2020

Photosynthetic semiconductor biohybrids for solar-driven biocatalysis

Photosynthetic semiconductor biohybrids integrate the best attributes of biological whole-cell catalysts and semiconducting nanomaterials. Enzymatic machinery enveloped in its native cellular environment offers exquisite product selectivity and low substrate activation barriers while semiconducting nanomaterials harvest light energy stably and efficiently. Here, we illustrate the evolution and advances of photosynthetic semiconductor biohybrids focusing on the conversion of CO 2 to value-added chemicals. We begin by considering the potential of this nascent field to meet global energy challenges while comparing it to alternate approaches. This is followed by a discussion of the advantageous coupling of electrotrophic organisms with light-active electrodes for solar-to-chemical conversion. We detail the dynamic investigation of photosensitized microorganisms creating direct light harvesting within unicellular organisms while describing complementary developments in the understanding of charge transfer mechanisms and cytoprotection. Lastly, we focus on trends and improvements needed in photosynthetic semiconductor biohybrids in order to address future challenges and enhance their widespread adoption for the production of solar chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Identification of a pathway for electron uptake in Shewanella oneidensis

Extracellular electron transfer (EET) could enable electron uptake into microbial metabolism for the synthesis of complex, energy dense organic molecules from CO 2 and renewable electricity. Theoretically EET could do this with an efficiency comparable to H 2 -oxidation but without the need for a volatile intermediate and the problems it causes for scale up. However, significant gaps remain in understanding the mechanism and genetics of electron uptake. For example, studies of electron uptake in electroactive microbes have shown a role for the Mtr EET complex in the electroactive microbe Shewanella oneidensis MR-1, though there is substantial variation in the magnitude of effect deletion of these genes has depending on the terminal electron acceptor used. This speaks to the potential for previously uncharacterized and/or differentially utilized genes involved in electron uptake. To address this, we screened gene disruption mutants for 3667 genes, representing ≈99% of all nonessential genes, from the S. oneidensis whole genome knockout collection using a redox dye oxidation assay. Confirmation of electron uptake using electrochemical testing allowed us to identify five genes from S. oneidensis that are indispensable for electron uptake from a cathode. Knockout of each gene eliminates extracellular electron uptake, yet in four of the five cases produces no significant defect in electron donation to an anode. This result highlights both distinct electron uptake components and an electronic connection between aerobic and anaerobic electron transport chains that allow electrons from the reversible EET machinery to be coupled to different respiratory processes in S. oneidensis. Homologs to these genes across many different genera suggesting that electron uptake by EET coupled to respiration could be widespread. These gene discoveries provide a foundation for: studying this phenotype in exotic metal-oxidizing microbes, genetic optimization of electron uptake in S. oneidensis; and genetically engineering electron uptake into a highly tractable host like E. coli to complement recent advances in synthetic CO2 fixation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A multi-omic characterization of the physiological responses to salt stress in Scenedesmus obliquus UTEX393

Scenedesmus obliquus UTEX393 is a promising microalgal candidate for sustainable biomanufacturing but its limited halotolerance hinders large-scale cultivation in saline environments. To investigate the molecular basis of salt stress responses, we conducted a comprehensive multi-omic analysis integrating genomics, transcriptomics, proteomics, lipidomics, metabolomics, and DNA affinity purification sequencing (DAP-seq). An improved nuclear genome assembly and annotation yielded 19,017 gene models and a 97% BUSCO completeness score, enabling construction of a genome-scale metabolic model. Comparing 15 ppt salinity stress to 5 ppt control, growth and productivity were significantly reduced, accompanied by widespread transcriptomic and proteomic changes. Transcriptomic analysis revealed downregulation of photosynthetic machinery and energy conservation genes, and upregulation of stress-responsive elements such as expansins, flavodoxins, and osmoprotectants. Lipidomic profiling showed accumulation of triacylglycerols (TAGs) and degradation of galactosyl lipids, consistent with a shift toward lipid biosynthesis to mitigate redox imbalance. Depletion of key polar metabolites and branched-chain amino acids suggested a rerouting of central carbon metabolism under stress. DAP-seq identified key transcription factors, including LHY1 and SPL12, that target central metabolic enzymes involved in redox balancing, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and malate dehydrogenase (MDH). These findings establish a regulatory-metabolic framework linking redox stress to lipid accumulation and reveal potential engineering targets to enhance salt tolerance. Overall, the multi-omic analysis supports the “overflow” hypothesis, where impaired photosynthesis results in excess reducing equivalents being diverted into TAG synthesis and highlights transcriptional regulators as candidates for improving algal robustness in brackish environments.

09 BIOMASS FUELS↗
DOE OSTI2025

Cell-free synthetic biology for natural product biosynthesis and discovery

Natural products have applications as biopharmaceuticals, agrochemicals, and other high-value chemicals. However, there are challenges in isolating natural products from their native producers (e.g. bacteria, fungi, plants). In many cases, synthetic chemistry or heterologous expression must be used to access these important molecules. The biosynthetic machinery to generate these compounds is found within biosynthetic gene clusters, primarily consisting of the enzymes that biosynthesise a range of natural product classes (including, but not limited to ribosomal and nonribosomal peptides, polyketides, and terpenoids). Cell-free synthetic biology has emerged in recent years as a bottom-up technology applied towards both prototyping pathways and producing molecules. Recently, it has been applied to natural products, both to characterise biosynthetic pathways and produce new metabolites. This review discusses the core biochemistry of cell-free synthetic biology applied to metabolite production and critiques its advantages and disadvantages compared to whole cell and/or chemical production routes. Specifically, we review the advances in cell-free biosynthesis of ribosomal peptides, analyse the rapid prototyping of natural product biosynthetic enzymes and pathways, highlight advances in novel antimicrobial discovery, and discuss the rising use of cell-free technologies in industrial biotechnology and synthetic biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Decoding substrate specificity determining factors in glycosyltransferase-B enzymes – insights from machine learning models

Substrate specificity is an essential characteristic of any enzyme's function and an understanding of the factors that determine this specificity is crucial for enzyme engineering. Unlike the structure of an enzyme which is directly impacted by its sequence, substrate specificity as an enzyme attribute involves a rather indirect relationship with sequence as it also depends on structural aspects that dictate substrate accessibility and active site dynamics. In this study, we explore the performance of classifier-based machine learning models trained on curated sequence and structural data for a class of glycosyltransferases (GTs), namely GT-Bs, to understand their substrate specificity determining factors. GTs enable the transfer of sugar moieties to other biomolecules such as oligosaccharides or proteins and are found in all kingdoms of life. In plants, GTs participate in the biosynthesis of plant cell wall biopolymers (e.g.: hemicelluloses and pectins) and are an integral part of the enzymatic machinery that enables the storage of carbon and energy as plant biomass. To elucidate the substrate specificity of uncharacterized GT-Bs, we constructed multi-label machine learning models (Support Vector Classifier, K-Nearest Neighbors, Gaussian Naïve-Bayes, Random Forest) that incorporate both sequence and structural features. These models achieve good predictive accuracies on test datasets. However, despite our use of structural information, we highlight that there is further scope for improvement in training these models to draw interpretable relationships between sequence, structure and substrate specificity determining motifs in GT-Bs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Adapting enzymes to improve their functionality in plants: why and how

Synthetic biology creates new metabolic processes and improves existing ones using engineered or natural enzymes. These enzymes are often sourced from cells that differ from those in the target plant organ with respect to, e.g. redox potential, effector levels, or proteostasis machinery. Non-native enzymes may thus need to be adapted to work well in their new plant context (‘plantized’) even if their specificity and kinetics in vitro are adequate. Hence there are two distinct ways in which an enzyme destined for use in plants can require improvement: In catalytic properties such as substrate and product specificity, kcat, and KM; and in general compatibility with the milieu of cells that express the enzyme. Continuous directed evolution systems can deliver both types of improvement and are so far the most broadly effective way to deliver the second type. Accordingly, in this review we provide a short account of continuous evolution methods, emphasizing the yeast OrthoRep system because of its suitability for plant applications. We then cover the down-to-earth and increasingly urgent issues of which enzymes and enzyme properties can — or cannot — be improved in theory, and which in practice are the best to target for crop improvement, i.e. those that are realistically improvable and important enough to warrant deploying continuous directed evolution. We take horticultural crops as examples because of the opportunities they present and to sharpen the focus.

Biochemistry & Molecular Biology↗
DOE OSTI2023

From BEYONDPLANCK to COSMOGLOBE: Preliminary WMAP Q -band analysis

We present the first application of the COSMOGLOBE analysis framework by analyzing nine-year WMAP time-ordered observations that uses similar machinery to that of BEYONDPLANCK for the Planck Low Frequency Instrument (LFI). We analyzed only the Q-band (41 GHz) data and report on the low-level analysis process based on uncalibrated time-ordered data to calibrated maps. Most of the existing BEYONDPLANCK pipeline may be reused for WMAP analysis with minimal changes to the existing codebase. The main modification is the implementation of the same preconditioned biconjugate gradient mapmaker used by the WMAP team. Producing a single WMAP Q1-band sample requires 22 CPU-hrs, which is slightly more than the cost of a Planck 44 GHz sample of 17 CPU-hrs; this demonstrates that a full end-to-end Bayesian processing of the WMAP data is computationally feasible. In general, our recovered maps are very similar to the maps released by the WMAP team, although with two notable differences. In terms of temperature, we find a ~2 μK quadrupole difference that most likely is caused by different gain modeling, while in polarization we find a distinct 2.5 μK signal that has been previously referred to as poorly measured modes by the WMAP team. In the COSMOGLOBE processing, this pattern arises from temperature-to-polarization leakage from the coupling between the CMB Solar dipole, transmission imbalance, and sidelobes. No traces of this pattern are found in either the frequency map or TOD residual map, suggesting that the current processing has succeeded in modeling these poorly measured modes within the assumed parametric model by using Planck information to break the sky-synchronous degeneracies inherent in the WMAP scanning strategy.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Nonadiabatic couplings from a variational excited state method based on constrained DFT

Excited Costrained Density Functional Theory (XCDFT) is a variational excited state method that extends ground state DFT to the computation of low-lying excited states. It borrows much of the machinery of Constrained DFT (CDFT) with a crucial difference: the constraint imposes a population of one electron in the Hilbert space spanned by the virtuals of a reference ground state. Here, we present theory and implementation for evaluating nonadiabatic coupling vectors (NACVs) between the first excited state computed with XCDFT and the ground state. Our NACVs are computed analytically using density functional perturbation theory with a formalism that is general enough that could be applied to CDFT diabatic states. We showcase the new method with pilot NACV calculations for the conical intersection in H 3 , the avoided crossing in selenoacrolein, and the NACV magnitudes in azobenzene. Despite complications from the nonorthogonality of the wavefunctions, XCDFT’s energy surfaces and NACVs reproduce benchmark values and respect known sum rules within a reasonable degree. This shows that XCDFT is a viable method for nonadiabatic dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

DFT-based QM/MM with Particle-Mesh Ewald for Direct, Long-Range Electrostatic Embedding

In this work, we present a DFT-based, QM/MM implementation with long-range electrostatic embedding achieved by direct real-space integration of the particle mesh Ewald (PME) computed electrostatic potential. The key transformation is the interpolation of the electrostatic potential from the PME grid to the DFT quadrature grid, from which integrals are easily evaluated utilizing standard DFT machinery. We provide benchmarks of the numerical accuracy with choice of grid size and real-space corrections, and demonstrate that good convergence is achieved while introducing nominal computational overhead. Furthermore, the approach requires only small modification to existing software packages, as is demonstrated with our implementation in the OpenMM and Psi 4 software. After presenting convergence benchmarks, we evaluate the importance of long-range electrostatic embedding in three solute/solvent systems modeled with QM/MM. Water and BMIM/BF 4 ionic liquid were considered as "simple" and "complex" solvents respectively, with water and p-phenylenediamine (PPD) solute molecules treated at QM level of theory. While electrostatic embedding with standard real-space truncation may introduce negligible error for simple systems such as water solute in water solvent, errors become more significant when QM/MM is applied to complex solvents such as ionic liquids. An extreme example is the electrostatic embedding energy for oxidized PPD in BMIM/BF 4 for which real-space truncation produces severe error even at 2-3 nm cutoff distances. This latter example illustrates that utilization of QM/MM to compute redox potentials within concentrated electrolytes/ionic media requires carefully chosen long-range electrostatic embedding algorithms, with our presented algorithm providing a general and robust approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Observation of conformational dynamics in single light-harvesting proteins from cryptophyte algae

Photosynthetic organisms use pigment–protein complexes to capture the sunlight that powers most life on earth. Within these complexes, the position of the embedded pigments is all optimized for light harvesting. At the same time, the protein scaffold undergoes thermal fluctuations that vary the structure, and, thus, photophysics, of the complexes. While these variations are averaged out in ensemble measurements, single-molecule spectroscopy provides the ability to probe these conformational changes. We used single-molecule fluorescence spectroscopy to identify the photophysical substates reflective of distinct conformations and the associated conformational dynamics in phycoerythrin 545 (PE545), a pigment–protein complex from cryptophyte algae. Rapid switching between photophysical states was observed, indicating that ensemble measurements average over a conformational equilibrium. A highly quenched conformation was also identified, and its population increased under high light. This discovery establishes that PE545 has the characteristics to serve as a photoprotective site. Finally, unlike homologous proteins from the evolutionarily related cyanobacteria and red algae, quenching was not observed upon photobleaching, which may allow for robust photophysics without the need for rapid repair or replacement machinery. Collectively, these observations establish the presence of a rich and robust set of conformational states of PE545. Cryptophytes exhibit particularly diverse energetics owing to the variety of microenvironments in which they survive, and the conformational states and dynamics reported here may provide photophysical flexibility that contributes to their remarkable ability to flourish under diverse conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

The physical chemistry of solar fuels catalysis

The demonstration of effective light-driven electrochemical water splitting at the surface of a TiO 2 electrode in the seminal 1972 Honda–Fujishima publication spurred global research efforts to understand this effect and design advanced systems for solar H 2 generation from water as a carbon-free and sustainable fuel. In the 50+ years since that discovery, research investigating approaches toward the catalytic generation of the so-called “solar fuels,” i.e., not only H 2 from water but also CO 2 reduction products and NH 3 from N 2 , has expanded dramatically in scope and scale. The development of new experimental and computational methods and construction and commissioning of large-scale facilities have paved the way for important insights into the machinery of natural photosynthesis, leading to a greater understanding of the complexity of light-to-chemical energy conversion with an exquisite temporal and spatial resolution. Finally, these studies have provided the foundation for biologically inspired molecular and hybrid designs with the goal to promote the photochemical steps critical to solar fuels generation while avoiding unproductive or unnecessary pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Iowa’s agriculture is losing its Goldilocks climate

The Iowa landscape is endowed with rich, deep, dark soils that have high water-holding capacity. Because most of the state’s land is flat or gently rolling, agriculture can be practiced with large, efficient machinery. Historically, Iowa’s average climate is characterized by a growing season of about five to six months with favorable sunshine and warm temperatures. Its crop-dormant season has low enough temperatures to prevent overwintering of detrimental pests and pathogens. The seasonal cycle of precipitation has a spring–summer maximum and a winter minimum that generally provide a sufficient and timely supply of water to support high crop densities without the need for irrigation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A partially disordered region connects gene repression and activation functions of EZH2

Enhancer of Zeste Homolog 2 (EZH2) is the catalytic subunit of Polycomb Repressive Complex 2 (PRC2), which minimally requires two other subunits, EED and SUZ12, for enzymatic activity. EZH2 has been traditionally known to mediate histone H3K27 trimethylation, a hallmark of silent chromatin. Emerging evidence indicates that EZH2 also activates gene expression in cancer cells in a context distinct from canonical PRC2. The molecular mechanism underlying the functional conversion of EZH2 from a gene repressor to an activator is unclear. In this work, we show that EZH2 harbors a hidden, partially disordered transactivation domain (TAD) capable of interacting with components of active transcription machinery, mimicking archetypal acidic activators. The EZH2 TAD comprises the SRM (Stimulation-Responsive Motif) and SANT1 (SWI3, ADA2, N-CoR, and TFIIIB 1) regions that are normally involved in H3K27 methylation. The crystal structure of an EZH2–EED binary complex indicates that the EZH2 TAD mediates protein oligomerization in a noncanonical PRC2 context and is entirely sequestered. The EZH2 TAD can be unlocked by cancer-specific EZH2 phosphorylation events to undergo structural transitions that may enable subsequent transcriptional coactivator binding. The EZH2 TAD directly interacts with the transcriptional coactivator and histone acetyltransferase p300 and activates gene expression in a p300-dependent manner in cells. The corresponding TAD may also account for the gene activation function of EZH1, the paralog of EZH2. Distinct kinase signaling pathways that are known to abnormally convert EZH2 into a gene activator in cancer cells can now be understood in a common structural context of the EZH2 TAD.

59 BASIC BIOLOGICAL SCIENCES↗